The combination of climate and its characteristics geohydrological have shaped this reserve as a major habitat of birds and marine swamp; is the main nesting site of the Flamingos in Mexico along with Ria Celestun.
Ria Lagartos is a place of great biological and ecological interest. Some studies shed partial results from more than 450 species of vertebrates and nearly 100 vascular plant species, including many that are under official protection; also is a critical ecological zone for the reproduction of 280 species of birds. It is the only Mexican wetlands designated under the Ramsar Convention.
The reserve is located in a transition zone climates; the western part (station Ria Lagartos) presents a semi-arid climate, and the eastern part (Station Cuyo) presents a warm-humid climate. It is made up of plains with gentle slopes and uniform. The reservation is located in the region geomorfica platform called Yucatec home limestone, which is part of the coastal plain of the Gulf of Mexico.
The creek has an elongated shape with east to west and with a length of approximately 40 km. Actually there are several systems connected by small lagoon channels.
The system of loopholes in the reserve consists of three bodies of water. The first of these stretches of the San Felipe mouth to mouth of the channel that separates it from the creek Ria Lagartos, and the second, the Ria Lagartos creek, which extends from vessel evaporation of the salt to La Angostura and the third The Angostura the eastern end of the lake called Flamingos.
In the southern part of the reservation there are some hillocks and springs, which has influenced the settlement of the population. The reservation belongs to the floristic province Yucatan Peninsula, Caribbean region of the kingdom Neotropical; flora of this region is of influence Antilles and the Florida peninsula. The physiography of the area of the reserve allows the existence of various types of habitat characterized by its proximity to the ocean, the lagoon or the mainland, based on this feature, vegetation is grouped as follows: submerged vegetation, coastal sand dunes, mangroves, low caducifolia, tular-carrizal-pasture and hillocks. These variations promote increasing the diversity of plants and animals.